Dear happy users of Galaxy,
We are running Galaxy locally. It's a very fine tool! By now
everything works fine, except when I try to run any GATK program. I
usually get this error message:
##### ERROR ----------------------------------------------------------
--------------------------------
##### ERROR A USER ERROR has occurred (version 1.3-14-g348f2db):
##### ERROR The invalid arguments or inputs must be corrected before
the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to
view allowable command-line arguments.
##### ERROR Visit our wiki for extensive documentation
http://www.broadinstitute.org/gsa/wiki
##### ERROR Visit our forum to view answers to commonly asked
questions http://getsatisfaction.com/gsa
##### ERROR
##### ERROR MESSAGE: The fasta file you specified
(/tmp/tmpp0oxJu/hg19) does not exist.
##### ERROR ----------------------------------------------------------
--------------------------------
my picard_index.loc line for the hg19 reference looks like this:
hg19 hg19 hg19 hg19
/drive1/galaxy/reference/hg19/sam_index/hg19_ref.fa gatk
also the bam file I am submitting to GATK has the reference genome
specified in it's attributes.
Could please anyone help me.
Thank you
Franzi

Hi Metge,
Thank you for your kind comments!
The GATK tool wrappers are still in an early beta stage of
development.
Because of this, we are not ready to support set-up in local instances
yet.
If you have functionality input for the version on our Test server,
general feedback is welcomed on the galaxy-dev@bx.psu.edu mailing
list.
Take care,
Jen
Galaxy team
--
Jennifer Jackson
http://usegalaxy.orghttp://galaxyproject.org/wiki/Support

Hi Franzi,
You have one too many hg19 in there. The fields go like:
<unique_build_id> <dbkey> <display_name> <fasta_file_path>
<valid_tool_suites>
so:
hg19 hg19 hg19
/drive1/galaxy/reference/hg19/sam_index/hg19_ref.fa gatk
But do note that these tool integrations are still undergoing active
development. Please report bugs if you encounter any.
Thanks for using Galaxy,
Dan